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How to run BIDS/ciftify workflow on scinet

In three simple steps

  1. Get you shiz into BIDS format
  2. Run the fmriprep (--anat) container
    • note: this is useful because it can be resubmitted if it times out more easily
  3. Run the fmriprep_ciftify container

1. Get you shiz into BIDS format

TBA but there's lots of help for this

2. Run the fmriprep (--anat) container

see examples/sbatch_fmriprep1.1.2_anat_p08.sh script for example code..

3. Run the fmriprep_ciftify container

see examples/sbatch_fmriprep_ciftify_p08.sh script for example code..

For example, what I did today with ds00003

getting it onto scinet using datalad

Now that we have datalad working..we can install one openfmri dataset

This bit installs the ds000003 folder structure and metadata into my $SCRATCH folder

singularity run -B $SCRATCH/datalad:/scratch /scinet/course/ss2018/3_bm/8_publicdataneuro/datalad-datalad-master-fullmaster.simg install -s ///openfmri/ds000003 /scratch/ds000003

This bit will actually pull the data for one subject into my scratch.

singularity run -B $SCRATCH/datalad:/scratch /scinet/course/ss2018/3_bm/8_publicdataneuro/datalad-datalad-master-fullmaster.simg get /scratch/ds000003/sub-01

running fmriprep anat

first I moved these script into my scinet home using git. Note: this is highly recommended

cd ${home}/code
git clone https://github.com/edickie/bids-on-scinet.git

note that as the progect progresses I will add new scripts to the repo and run them using ...

cd ${home}/code/bids-on-scinet
git pull
mkdir $SCRATCH/sing_home
sbatch ~/code/bids-on-scinet/examples/sbatch_fmriprep1.1.2_anat_p08.sh

I will them check if my job ran using:

squeue -u $USER

now check to make sure that this step is done or near complete..

First (easy way to check) is to look for the words "no errors" in you fmriprep reports

ALSO NOTE: if this step times out you can restart it..

When things time out there is usually a IsRunning.lh+rh in the subjects output for example this output from

cd ${SCRATCH}/bids_outputs/ds000003/fmriprep_p08/freesurfer/sub-02/scripts
ls

gave me this output

edickie@nia-login07:/scratch/a/arisvoin/edickie/bids_outputs/ds000003/fmriprep_p08/freesurfer/sub-02/scripts$ ls -lrt
total 2048
-rw-rw-r-- 1 edickie arisvoin     58 Aug  2 15:58 build-stamp.txt
-rw-rw-r-- 1 edickie arisvoin   7983 Aug  2 15:58 recon-all.env.bak
-rw-rw-r-- 1 edickie arisvoin      1 Aug  2 16:11 patchdir.txt
-rw-rw-r-- 1 edickie arisvoin     58 Aug  2 16:11 lastcall.build-stamp.txt
-rw-rw-r-- 1 edickie arisvoin   7836 Aug  2 16:11 recon-all.env
-rw-rw-r-- 1 edickie arisvoin    360 Aug  2 16:11 IsRunning.lh+rh
-rwxrwxr-x 1 edickie arisvoin 327555 Aug  2 16:11 recon-all.local-copy
-rw-rw-r-- 1 edickie arisvoin    616 Aug  2 16:18 recon-all-status.log
-rw-rw-r-- 1 edickie arisvoin   2871 Aug  2 16:18 recon-all.cmd
-rw-rw-r-- 1 edickie arisvoin 102921 Aug  2 17:32 recon-all.log

To rerun if would delete the IsRunning.* file and resubmit the script

rm IsRunning.lh+rh
cd $SCRATCH/sing_home
sbatch ~/code/bids-on-scinet/examples/sbatch_fmriprep1.1.2_anat_p08.sh

running the rest of ciftify

Before we start, we should use git to pull in the newest version of our scripts. (Which, I assume, we have been busy writing...)

cd ${home}/code/bids-on-scinet
git pull

submit them to the queue

cd $SCRATCH/sing_home
sbatch ~/code/bids-on-scinet/examples/sbatch_fmriprep_ciftify_p08.sh